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- PDB-8vgd: Complex of ExbD with D-box peptide: Tetragonal form -

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Basic information

Entry
Database: PDB / ID: 8vgd
TitleComplex of ExbD with D-box peptide: Tetragonal form
Components
  • Biopolymer transport protein ExbD
  • GLN-PRO-ILE-SER-VAL-THR-MET-VAL-THR
KeywordsTRANSPORT PROTEIN / TonB / TonB-dependent transport / bacterial motor
Function / homology
Function and homology information


receptor-mediated bacteriophage irreversible attachment to host cell / colicin transport / energy transducer activity / cell envelope / cobalamin transport / siderophore transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / transmembrane transporter complex / transmembrane transporter activity ...receptor-mediated bacteriophage irreversible attachment to host cell / colicin transport / energy transducer activity / cell envelope / cobalamin transport / siderophore transport / intracellular monoatomic cation homeostasis / plasma membrane protein complex / transmembrane transporter complex / transmembrane transporter activity / cell outer membrane / transmembrane transport / protein transport / outer membrane-bounded periplasmic space / intracellular iron ion homeostasis / protein domain specific binding / membrane / plasma membrane
Similarity search - Function
TonB polyproline region / TonB C-terminal domain profile. / Gram-negative bacterial TonB protein / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB/TolA, C-terminal / TonB system transport protein ExbD type-1 / Biopolymer transport protein ExbD/TolR / Biopolymer transport protein ExbD/TolR
Similarity search - Domain/homology
Biopolymer transport protein ExbD / Protein TonB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsLoll, P.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Discovery and structural characterization of the D-box, a conserved TonB motif that couples an inner-membrane motor to outer-membrane transport.
Authors: Loll, P.J. / Grasty, K.C. / Shultis, D.D. / Guzman, N.J. / Wiener, M.C.
History
DepositionDec 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation / pdbx_related_exp_data_set / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Biopolymer transport protein ExbD
B: Biopolymer transport protein ExbD
P: GLN-PRO-ILE-SER-VAL-THR-MET-VAL-THR


Theoretical massNumber of molelcules
Total (without water)19,4523
Polymers19,4523
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-19 kcal/mol
Surface area8070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.010, 49.010, 62.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Biopolymer transport protein ExbD


Mass: 9238.591 Da / Num. of mol.: 2 / Fragment: periplasmic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: exbD, EIMP300_23080 / Plasmid: pETHSUL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8S0FLD5
#2: Protein/peptide GLN-PRO-ILE-SER-VAL-THR-MET-VAL-THR


Mass: 975.159 Da / Num. of mol.: 1 / Fragment: D-box peptide / Source method: obtained synthetically / Details: D-box peptide from TonB / Source: (synth.) Escherichia coli (E. coli) / References: UniProt: P02929
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.39 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 5.8
Details: 2M ammonium sulfate in 0.1 M sodium citrate, pH 5.8; microbatch under Al's oil

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92011 Å / Relative weight: 1
ReflectionResolution: 1.42→26.4 Å / Num. obs: 27989 / % possible obs: 100 % / Redundancy: 14.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.083 / Net I/σ(I): 13.6
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.42-1.465.06720290.275.2531
1.46-1.53.25820140.4783.3791
1.5-1.542.23619760.6522.3191
1.54-1.591.76518950.7351.831
1.59-1.641.25418470.8441.3011
1.64-1.70.97917670.8971.0151
1.7-1.760.72617330.9440.7531
1.76-1.830.50316420.9790.5221
1.83-1.910.29915870.9910.311
1.91-2.010.21515030.9930.2231
2.01-2.120.15114570.9950.1571
2.12-2.250.11513800.9970.121
2.25-2.40.09512790.9970.0991
2.4-2.590.08112090.9980.0841
2.59-2.840.07411100.9980.0771
2.84-3.180.0669950.9980.0691
3.18-3.670.0618880.9990.0631
3.67-4.490.0587610.9990.061
4.49-6.350.0595850.9970.0611
6.35-26.40.0733320.9970.0761

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→24.63 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.204 --
Rwork0.187 --
obs-26548 100 %
Refinement stepCycle: LAST / Resolution: 1.42→24.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1201 0 0 50 1251

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